It may be that you haven't lost any real bottom end but the mods you preformed improved the top end such that the bottom end now seems to be lacking. You have shifted the power band into the upper RPM range. The jet size you chose seems a little excessive for just a air filter change. you may be able to achieve a better balance by lowering the main jet and going up a touch on the pilot jet. There's no set rule on jet size when altering air/fuel. it's all trial and error.
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